Rants, raves (and occasionally considered opinions) on phyloinformatics, taxonomy, and biodiversity informatics. For more ranty and less considered opinions, see my Twitter feed.ISSN 2051-8188 View this blog in Magazine View.

Thursday, December 02, 2010

Linking taxonomic databases to the primary literature: BHL and the Australian Faunal Directory

Continuing my hobby horse of linking taxonomic databases to digitised literature, I've been working for the last couple of weeks on linking names in the Australian Faunal Directory (AFD) to articles in the Biodiversity Heritage Library (BHL). AFD is a list of all animals known to occur in Australia, and it provides much of the data for the recently released Atlas of Living Australia. The data is available as series of CSV files, and these contain quite detailed bibliographic references. My initial interest was in using these to populate BioStor with articles, but it seemed worthwhile to try and link the names and articles together. The Atlas of Living Australia links to BHL, but only via a name search showing BHL items that have a name string. This wastes valuable information. AFD has citations to individual books and articles that relate to the taxonomy of Australian animals — we should treat that as first class data.

So, I cobbled together the CSV files, some scripts to extract references, ran them through the BioStor and bioGUID OpenURL resolvers, and dumped the whole thing in a CouchDB database. You can see the results at Australian Faunal Directory on CouchDB.

The site is modelled on my earlier experiment with putting the Catalogue of Life on CouchDB. It's still rather crude, and there's a lot of stuff I need to work on, but it should illustrate the basic idea. You can browse the taxonomic hierarchy, view alternative names for each taxon, and see a list of publications related to those names. If a publication has been found in BioStor then the site displays a thumbnail of the first page, and if you click on the reference you see a simple article viewer I wrote in Javascript.

For PDFs I'm experimenting with using Google's PDF viewer (the inspiration for the viewer above):

How it was madeAlthough in principle linking AFD to BHL via BioStor was fairly straight forward, these are lots of little wrinkles, such as errors in bibliographic metadata, and failure to parse some reference strings. To help address this I created a public group on Mendeley where all the references I've extracted are stored. This makes it easy to correct errors, add identifiers such as DOIs and ISSNs, and upload PDFs. For each article a reference to the original record in AFD is maintained by storing the AFD identifier (a UUID) as a keyword.

The taxonomy and the mapping to literature is stored in a CouchDB database, which makes a lot of things (such as uploading new versions of documents) a breeze.

It's about the linksThe underlying motivation is that we are awash in biodiversity data and digitisation projects, but these are rarely linked together. And it's more than just linking, it's bring the data together so that we can compute over it. That's when things will start to get interesting.